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Sample GSM62237 Query DataSets for GSM62237
Status Public on Jun 25, 2005
Title wt 3N vs. wt 3H
Sample type RNA
 
Channel 1
Source name wt 3H
Organism Caenorhabditis elegans
Characteristics wt 3H
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name wt 3N
Organism Caenorhabditis elegans
Characteristics wt 3N
Extracted molecule total RNA
Label Cy5
 
 
Description Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-03/27035.gif; format: GIF
Data processing Value is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Jun 24, 2005
Last update date Nov 23, 2005
Contact name Min Jiang
E-mail(s) [email protected]
Phone 650-725-7612
Fax 650-725-7739
Organization name Stanford University
Street address -
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL2569
Series (1)
GSE2836 Hypoxia response

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
LOG_RAT2N_MEAN Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2
VALUE same as UNF_VALUE but with flagged values removed
UNF_VALUE Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN LOG_RAT2N_MEAN VALUE UNF_VALUE
1 7249 9791 62 114 7187 9677 7014 8458 74 117 6952 8344 0 0 4290 6535 57 44 98 100 96 100 16864 15296 .743 1.346 1.2 3.035 1.269 8.431 80 546 1.335 .97 110 1950 20060 84 95 105 116 0 11001 128 10873 1.513 9503 9375 .661 1.349 .597 .431 .431
2 5766 5543 65 113 5701 5430 6501 5852 72 116 6436 5739 0 0 2475 2236 45 44 100 100 100 100 11131 12175 1.05 .952 .892 1.13 .948 .856 52 283 .904 .97 80 2120 20070 87 95 124 132 0 6228 127 6101 1.07 6575 6448 .934 1.002 .098 .003 .003
3 419 321 62 96 357 225 407 319 65 102 345 223 0 0 133 90 20 36 100 100 100 100 582 568 1.587 .63 .646 .682 .642 .302 52 343 .56 .85 90 2270 20060 85 94 138 147 0 361 108 253 .708 358 251 1.412 .726 -.498 -.461 -.461
4 1401 1063 68 103 1333 960 1643 1150 81 110 1575 1047 0 0 693 531 48 41 100 100 100 100 2293 2622 1.389 .72 .665 .76 .711 .324 52 345 .673 .96 90 2440 20050 84 93 155 164 0 1194 116 1079 .809 1292 1176 1.236 .747 -.305 -.421 -.421
5 10290 9013 65 104 10225 8909 13385 10719 75 108 13320 10615 0 0 5476 4947 36 37 100 100 100 100 19134 23935 1.148 .871 .797 .951 .901 .402 80 434 .858 .97 100 2600 20050 84 94 171 181 0 10127 117 10010 .979 12044 11927 1.021 .895 -.031 -.159 -.159
6 1239 1064 67 108 1172 956 1094 863 72 107 1027 755 0 0 963 694 27 33 100 100 100 100 2128 1782 1.226 .816 .735 .994 .869 .564 32 231 .747 .97 70 2760 20060 86 93 188 195 0 1196 121 1074 .917 970 848 1.091 .826 -.126 -.276 -.276
7 10399 12881 60 104 10339 12777 11619 13776 67 110 11559 13672 0 0 4695 5908 27 38 100 100 100 100 23116 25231 .809 1.236 1.183 1.666 1.255 2.032 52 311 1.203 .98 80 2920 20060 86 94 204 212 0 14473 117 14356 1.389 15479 15362 .72 1.329 .474 .41 .41
8 348 398 56 116 292 282 291 355 59 122 235 239 0 0 201 178 18 42 96 96 96 90 574 474 1.035 .966 1.017 1.115 .956 .614 32 170 .799 .87 60 3080 20060 87 93 221 227 0 447 130 317 1.085 399 269 .922 1.143 .118 .192 .192
9 1611 553 62 115 1549 438 1602 570 67 119 1540 455 0 0 378 167 28 40 100 98 100 97 1987 1995 3.537 .283 .295 .282 .281 .097 80 503 .272 .92 110 3240 20060 84 95 234 245 0 621 129 492 .318 640 511 3.148 .332 -1.654 -1.591 -1.591
10 954 440 64 111 890 329 1028 427 74 114 964 316 0 0 502 193 35 36 98 95 95 88 1219 1280 2.705 .37 .328 .659 .356 1.226 80 412 .333 .89 100 3400 20070 86 96 251 261 0 494 125 370 .415 480 355 2.408 .368 -1.268 -1.441 -1.441
11 4571 3043 64 112 4507 2931 4912 3451 71 115 4848 3339 0 0 1896 1313 36 39 98 100 98 99 7438 8187 1.538 .65 .689 .843 .671 1.202 120 522 .626 .95 120 3570 20060 84 96 267 279 0 3419 126 3293 .731 3878 3752 1.369 .774 -.453 -.37 -.37
12 814 721 64 124 750 597 791 731 68 128 727 607 0 0 185 165 21 41 100 100 100 100 1347 1334 1.256 .796 .835 .828 .812 .257 52 324 .711 .9 90 3720 20050 84 93 283 292 0 810 139 671 .894 821 682 1.118 .938 -.161 -.092 -.092
13 6879 3902 66 125 6813 3777 7240 4033 99 137 7174 3908 0 0 2596 1277 233 70 98 100 98 100 10590 11082 1.804 .554 .545 .68 .555 .698 52 373 .511 .95 90 3880 20050 84 93 299 308 0 4384 140 4244 .623 4531 4391 1.605 .612 -.683 -.708 -.708
14 310 254 63 129 247 125 313 257 67 129 250 128 0 0 124 68 21 37 96 82 94 78 372 378 1.976 .506 .512 .968 .552 2.28 52 308 .409 .71 80 4050 20060 86 94 317 325 0 285 145 140 .569 289 144 1.759 .575 -.814 -.798 -.798
15 400 302 65 122 335 180 399 279 69 125 334 157 0 0 102 82 22 37 100 100 100 94 515 491 1.861 .537 .47 .576 .542 .272 52 297 .436 .78 80 4200 20050 85 93 332 340 0 339 137 202 .604 313 176 1.656 .528 -.728 -.921 -.921
16 572 517 68 114 504 403 529 507 73 117 461 393 0 0 211 160 25 36 100 100 100 100 907 854 1.251 .8 .852 .86 .813 .358 52 287 .689 .88 80 4360 20040 84 92 348 356 0 581 128 453 .898 570 442 1.113 .958 -.155 -.062 -.062
17 10983 6936 68 119 10915 6817 12788 8229 75 128 12720 8110 0 0 4444 2705 32 53 100 100 100 100 17732 20830 1.601 .625 .638 .641 .618 .149 52 379 .602 .98 90 4520 20040 83 92 363 372 0 7793 134 7660 .702 9246 9112 1.425 .716 -.511 -.481 -.481
18 1390 989 68 127 1322 862 1176 886 143 169 1108 759 0 0 618 512 314 203 100 94 84 71 2184 1867 1.534 .652 .685 .649 .669 .278 52 317 .662 .94 90 4690 20010 80 89 380 389 0 1111 143 969 .733 996 853 1.365 .77 -.449 -.378 -.378
19 2166 1813 64 128 2102 1685 2330 1847 98 148 2266 1719 0 0 746 645 192 137 98 100 97 100 3787 3985 1.247 .802 .759 .842 .76 .298 80 493 .777 .96 110 4840 20050 83 94 394 405 0 2037 144 1893 .901 2075 1931 1.11 .852 -.151 -.23 -.23
20 984 669 62 113 922 556 1081 683 65 119 1019 570 0 0 371 229 21 37 98 100 98 100 1478 1589 1.658 .603 .559 .775 .605 1.091 80 427 .547 .93 100 5010 20040 83 93 412 422 0 752 127 625 .678 767 640 1.476 .629 -.562 -.67 -.67

Total number of rows: 21888

Table truncated, full table size 4985 Kbytes.




Supplementary data files not provided
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